Hi, I've divided the cell cycle data in 4 subsets (cc_subset_x in test_data folder) based on complete linkage hierarchical clustering (using Pearson's correlation as similarity measure). There's cell cycle genes in all 4 sets, but subset_3 has most of them (42/87, see .bgo files). Please be aware that when running LeMoNe and successors on these subsets, you make the assumption that not many genes of different subsets ought to end up in the same module. Another preprocessing step that I would like you to consider is to mean-normalize the genewise expression profiles (mean 0, unit stdev) before running LeMoNe, so that genes with similar behavior but different amplitude would end up in the same module. Currently, the expression profiles are not mean-normalized, it's better to provide this option in the program... Cheers, Steven -- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3810 fax: +32 9 331 3809 email: stmae@psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================